#if !defined(READ_OPTIONS_H)
#define READ_OPTIONS_H


#include "std_options.h"
#include <vector>
#include <string>
//________________________________________________________________________________________
// 
// 		read_options
//________________________________________________________________________________________
class prog_options : public t_std_options
{
private:
public:
	prog_options():
		t_std_options(
							// description
							"Calculating founders from sparsely sequenced genotypes using dynamic programming. "
							"Defaults to haploid mode unless --diploid or both --diploid --haploid are specified.\n",
							// program usage
							"--allele_file PATH --call_file PATH \n"
							"--penalty FLOAT [--diploid --haploid  --exclude_regions_gff PATH  --exclude_regions PATH --allele_file PATH] \n"
							"[options] ",						
							// version
							"1.0 01/04/2011",
							// use summary file
							true
			),
			penalty(0),
			homozygous_match(2),
			heterozygous_match(3),
			diploid(false),
			haploid(false)
		{}
	std::vector<std::string>	allele_filenames;
	std::vector<std::string>	call_filenames;
	std::vector<std::string>	exclude_regions_gff_filenames;
	std::vector<std::string>	exclude_regions_filenames;
	std::string                 call_file_to_name_regex;
	std::string					founders_output_file;
	unsigned					penalty  ;
	unsigned					homozygous_match  ;
	unsigned					heterozygous_match  ;
	bool						diploid;
	bool						haploid;

};

bool read_options(prog_options& opt, int argc, char *argv[]);
#endif



